vcftobedpe's output has one-based START coordinates instead of one-based

Svtools' vcftobedpe tool produces one-based START coordinates in bedpe output, instead of zero-based coordinates that bedpe requires. I came across this (major) bug as bedtools' pairtopair would not work as expected even if same bedpe file as input to -a and -b. This is because bedpe is not in valid bedpe format, and this is a major problem especially for SV calls whose CIPOS/CIEND is 0,0.

From quick look, concerning code is this: https://github.com/hall-lab/svtools/blob/6a6a7b059df196ec49de6cd0b8ff816942f9055a/svtools/vcftobedpeconverter.py#L80-L82

And here are the test files and command I used. Note that bedpe's START coordinates are one-based.

Command used: svtools vcftobedpe -i test.vcf -o out.bedpe
Test vcf file:

##fileformat=VCFv4.1
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  sample
chr1    839442  MantaDEL:123157:0:0:0:0:0   CACCTAGACACACACTCCTGGACACACACACCTAGACACACACACCTGGACAAACACA  CT  139 PASS    END=839499;SVTYPE=DEL;SVLEN=-57;CIGAR=1M1I57D   GT:FT:GQ:PL:PR:SR   0/1:PASS:86:189,0,83:1,0:8,5
chr1    1477835 MantaDEL:123205:0:1:0:1:0   AGCTGGGATTACAGGCACGCGCCACCACGCCTGGCTAATGTTGTATTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCTAACTCCCGACCTCAGGTGATCCACCCGCCTCGGCCTCTCAAACT  A   27  PASS    END=1477968;SVTYPE=DEL;SVLEN=-133;CIGAR=1M133D;CIPOS=0,34;HOMLEN=34;HOMSEQ=GCTGGGATTACAGGCACGCGCCACCACGCCTGGC   GT:FT:GQ:PL:PR:SR   0/1:PASS:27:77,0,324:18,0:32,3
chr1    1565630 MantaDUP:TANDEM:123223:0:1:0:0:0    G   <DUP:TANDEM>    94  PASS    END=1565727;SVTYPE=DUP;SVLEN=97;CIPOS=0,1;CIEND=0,1;HOMLEN=1;HOMSEQ=T   GT:FT:GQ:PL:PR:SR   0/1:PASS:94:144,0,772:27,0:53,9
chr1    1595101 MantaDEL:123214:0:0:0:1:0   TGACAGAGAGAGGCAGAGAGAGAGAGAGAGAGACAGACACAGAGAGAGCAGAACAGGGAGAAACAGAGAGACAGAGAGCGAGA T   238 MaxDepth    END=1595183;SVTYPE=DEL;SVLEN=-82;CIGAR=1M82D;CIPOS=0,2;HOMLEN=2;HOMSEQ=GA   GT:FT:GQ:PL:PR:SR   0/1:PASS:238:288,0,341:10,0:41,10

Output bedpe file


##fileformat=BEDPE
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=POS,Number=1,Type=Integer,Description="Position of the variant described in this record">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM_A    START_A END_A   CHROM_B START_B END_B   ID  QUAL    STRAND_A    STRAND_B    TYPE    FILTER  NAME_A  REF_A   ALT_A   NAME_B  REF_B   ALT_B   INFO_A  INFO_B  FORMAT  sample
chr1    839442  839442  chr1    839499  839499  MantaDEL:123157:0:0:0:0:0   139.0   +   -   DEL PASS    MantaDEL:123157:0:0:0:0:0   CACCTAGACACACACTCCTGGACACACACACCTAGACACACACACCTGGACAAACACA  CT  .   .   .   SVTYPE=DEL;POS=839442;SVLEN=-57;END=839499  .   GT:FT:GQ:PL:PR:SR   0/1:PASS:86:189,0,83:1,0:8,5
chr1    1477835 1477869 chr1    1477968 1477968 MantaDEL:123205:0:1:0:1:0   27.0    +   -   DEL PASS    MantaDEL:123205:0:1:0:1:0   AGCTGGGATTACAGGCACGCGCCACCACGCCTGGCTAATGTTGTATTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCTAACTCCCGACCTCAGGTGATCCACCCGCCTCGGCCTCTCAAACT  A   .   .   .   SVTYPE=DEL;POS=1477835;SVLEN=-133;END=1477968;CIPOS=0,34    .   GT:FT:GQ:PL:PR:SR   0/1:PASS:27:77,0,324:18,0:32,3
chr1    1565630 1565631 chr1    1565727 1565728 MantaDUP:TANDEM:123223:0:1:0:0:0    94.0    +   -   DUP PASS    MantaDUP:TANDEM:123223:0:1:0:0:0    G   <DUP:TANDEM>    .   .   .   SVTYPE=DUP;POS=1565630;SVLEN=97;END=1565727;CIPOS=0,1;CIEND=0,1 .   GT:FT:GQ:PL:PR:SR   0/1:PASS:94:144,0,772:27,0:53,9
chr1    1595101 1595103 chr1    1595183 1595183 MantaDEL:123214:0:0:0:1:0   238.0   +   -   DEL MaxDepth    MantaDEL:123214:0:0:0:1:0   TGACAGAGAGAGGCAGAGAGAGAGAGAGAGAGACAGACACAGAGAGAGCAGAACAGGGAGAAACAGAGAGACAGAGAGCGAGA T   .   .   .   SVTYPE=DEL;POS=1595101;SVLEN=-82;END=1595183;CIPOS=0,2  .   GT:FT:GQ:PL:PR:SR   0/1:PASS:238:288,0,341:10,0:41,10

hall-lab / svtools

vcftobedpe's output has one-based START coordinates instead of one-based #301